Balancing scientific interests and the rights of participants in designing a recall by genotype study

Recall by genotype (RbG) studies aim to better understand the phenotypes that correspond to genetic variants of interest, by recruiting carriers of such variants for further phenotyping. RbG approaches pose major ethical and legal challenges related to the disclosure of possibly unwanted genetic information. The Cooperative Health Research in South Tyrol (CHRIS) study is a longitudinal cohort study based in South Tyrol, Italy. Demand has grown for CHRIS study participants to be enrolled in RbG studies, thus making the design of a suitable ethical framework a pressing need. We here report upon the design of a pilot RbG study conducted with CHRIS study participants. By reviewing the literature and by consulting relevant stakeholders (CHRIS participants, clinical geneticists, ethics board, GPs), we identified key ethical issues in RbG approaches (e.g. complexity of the context, communication of genetic results, measures to further protect participants). The design of the pilot was based on a feasibility assessment, the selection of a suitable test case within the ProtectMove Research Unit on reduced penetrance of hereditary movement disorders, and the development of appropriate recruitment and communication strategies. An empirical study was embedded in the pilot study with the aim of understanding participants’ views on RbG. Our experience with the pilot study in CHRIS allowed us to contribute to the development of best practices and policies for RbG studies by drawing recommendations: addressing the possibility of RbG in the original consent, implementing tailored communication strategies, engaging stakeholders, designing embedded empirical studies, and sharing research experiences and methodology

Genome-wide association study identifies multiple genetic loci for activated partial thromboplastin time and prothrombin time

Background: Activated partial thromboplastin time (aPTT) and prothrombin time (PT) are commonly used to screen for coagulation factor deficiencies. Shorter aPTT is also a risk marker for incident and recurrent venous thromboembolism (VTE). Genetic factors influencing aPTT and PT are not well understood. So far only one genome-wide association study (GWAS) has been reported for aPTT in 1,477 participants and none for PT. Methods: We conducted a GWAS for the aPTT in 9,240 European Americans (EAs) from the Atherosclerosis Risk in Communities (ARIC) study and for PT in 1,221 EAs from the Genetic Study of Three Population Microisolates in South Tyrol (MICROS). Replication was assessed by in silico analysis in MICROS (aPTT, n=1,215) and the Lothian Birth Cohorts (LBC) (LBC1936 (aPTT and PT, n=925-989), LBC1921 (aPTT, n=445)), and by de novo genotyping in the Caerphilly study (aPTT, n=882). Subjects on anticoagulants were excluded. Genotyping was conducted with the Affymetrix single nucleotide polymorphism (SNP) array 6.0 or Illumina HumanHap300/370 and imputed to 2.5 million HapMap SNPs. SNPs with imputation quality score < 0.3 or minor allele frequencies 1% were excluded from data analysis. The imputed SNP dosages were analyzed in linear regression adjusted for age, sex, and field center, where applicable. Results: Five loci were associated with aPTT at genome-wide significance of p<5x10-8 that have not been previously reported: F5 (1q23, top SNP rs9332701, missense, β (effect size associated with one copy increase in minor allele)=0.54, p=3.7x10-8), F11 (4q35, rs1593, intronic, β =0.54 and 0.36, p=1.25x10-17 and 2.0x10-8 before and after adjusting for known variants in F11), NSD1 (5q35.2-q35.3, rs11950938, intronic, β =1.00 and 1.21, p=1.11x10-15 and 1.5x10-22 before and after adjusting for known variants in F12 of the same region), C6orf10 (6p21.3, rs2050190, intronic, β =-0.25, p=1.3x10-8), and ABO (9q34.1-q34.2, rs8176704, intronic, tag for A2 group, β =0.19 and 0.89, p=0.02 and 4.3x10-24 before and after adjusting for O blood group). Three of the five loci replicated in at least one replication sample and the other two were directionally consistent in 3 replication samples. Furthermore, meta-analysis pooling the discovery and replication GWAS samples yielded two additional independent loci at chromosomes 1q23 (F5, best SNP rs6028, coding-synonymous, β =0.23, p=5.97x10-9) and 15q25.3 (AGBL1, rs2469184, intronic, β =0.16, p= 4.24x10-8), with consistent associations across studies. The signals at the F5 region were not due to FV Leiden (rs6025, p=0.46 in ARIC). We also confirmed previously reported loci in KNG1, HRG, F11, F12, and ABO (O group). For PT, novel associations from two gene regions reached genome-wide significance in MICROS: F7 (top SNP rs3093253, within an exon but not translated, β =-5.44, p=8.2x10-19) and PROCR (rs6060244, near PROCR, β =4.11, p=3.5x10-9). Both loci replicated in LBC1936. Conclusions: In this large GWAS, six of the nine novel loci associated with the aPTT and PT are coagulation-related and the other three (NSD1, C6orf10, and AGBL1) are new candidate genes not directly involved in coagulation. The C6orf10 gene interacts with TNF-a at the transcription level and was previously associated with inflammatory diseases. These findings may be relevant to the prevention and treatment of coagulation disorders including VTE

New gene functions in megakaryopoiesis and platelet formation

Platelets are the second most abundant cell type in blood and are essential for maintaining haemostasis. Their count and volume are tightly controlled within narrow physiological ranges, but there is only limited understanding of the molecular processes controlling both traits. Here we carried out a high-powered meta-analysis of genome-wide association studies (GWAS) in up to 66,867 individuals of European ancestry, followed by extensive biological and functional assessment. We identified 68 genomic loci reliably associated with platelet count and volume mapping to established and putative novel regulators of megakaryopoiesis and platelet formation. These genes show megakaryocyte-specific gene expression patterns and extensive network connectivity. Using gene silencing in Danio rerio and Drosophila melanogaster, we identified 11 of the genes as novel regulators of blood cell formation. Taken together, our findings advance understanding of novel gene functions controlling fate-determining events during megakaryopoiesis and platelet formation, providing a new example of successful translation of GWAS to function